MolNFT v1 · #104304 · protein
Crystal structure of a putative neuraminidase (BACCAC_01090) from bacteroides caccae atcc 43185 at 1.90 a resolution (psi community target)
4Q6K · BNR/ASP-box repeat protein: “Crystal structure of a putative neuraminidase (BACCAC_01090) from bacteroides caccae atcc 43185 at 1.90 a…”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.73). MolNFT v1 #104304 on…
- PDB
- 4Q6K
- Type
- protein
- Length
- 2,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BNR/ASP-box repeat protein
- UniProt
- A5ZDY0
- Ligands
- K
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | BNR/ASP-box repeat protein | protein | 523 | 6% helix, 45% strand | A5ZDY0 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.73 | 0.80 | 58 | EDO |
| 2 | 729 | 0.71 | 0.77 | 52 | empty |
| 3 | 318 | 0.69 | 0.83 | 29 | EDO |
| 4 | 335 | 0.67 | 0.81 | 28 | EDO |
| 5 | 324 | 0.66 | 0.81 | 28 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 1545 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1541 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
Compared structures
- 4Q6K · Crystal structure of a putative neuraminidase (BACCAC_01090) from Bacteroides caccae ATCC… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A5ZDY0
- Elsewhere: RCSB PDB 4Q6K · PDBe 4Q6K · UniProt A5ZDY0
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